Patients with diabetes were enrolled into a telemonitoring programme. They were offered the choice of collecting their health data either by using Near Field Communication (NFC) enabled mobile phones equipped with a dedicated application (App), or by means of a web-browser based user interface (Web). At the end of the study, each patient was categorized as belonging to either the App or Web group, based on the proportion of data they had transmitted using each method. Of the 403 patients, there were 291 in the App group and 112 in the Web group. The two groups were similar in their demographics, except for gender distribution where 68% of men preferred using the App method in contrast to 95% for women (P < 0.001). Kaplan-Meier analysis showed a steady decline of the compliance rate for both groups, at a similar rate during the first year. It also showed a more rapid decline of the compliance rate thereafter for the Web group, which resulted in a significantly higher rate for the App group over the whole observation period (P = 0.03). We conclude that different types of data acquisition technologies may have an important effect on patients' willingness to participate in telehealth programmes in the long-term.